Tag: PPI

Med-Life Discoveries, LP (MLD) is a Canadian biopharmaceutical company dedicated to advancing a therapy to reduce symptoms for a devastating pediatric rare disease, Rhizomelic chondrodysplasia punctata (RCDP), which causes significant physical and neurological delays in children who inherit it.  MLD has received a no objection letter (NOL) from Health Canada…

Behavioral testing After undergoing a four-day training program, the mice were subjected to a positioning cruise experiment on the fifth day. The experiment involved comparing the escape latency and swimming distance in the quadrant opposite to the platform between the WD group and the control group. The findings indicated that…

NEW YORK – Since its introduction in 2018, DeepMind’s AlphaFold program has become a key tool in biological research, allowing scientists to predict protein structures with high accuracy based on their amino acid sequences. More recently, researchers have begun using AlphaFold and its newer iteration, AlphaFold2, for protein-protein interaction (PPI)…

Abstract De novo protein design enhances our understanding of the principles that govern protein folding and interactions, and has the potential to revolutionize biotechnology through the engineering of novel protein functionalities. Despite recent progress in computational design strategies, de novo design of protein structures remains challenging, given the vast size…

Screening for pivotal genes in diabetic peripheral neuropathy In screening the DEGs, a total of 6 DPN samples and 6 control samples were included in the GEO dataset GSE95849, and this dataset was normalised. A principal component analysis (PCA) of GSE95849 was conducted to demonstrate clustering using scatter plots. Each…

Microarray-based expression analysis and GEO database analysis The DLBCL-related miRNA expression profiles of GSE29493 and GSE40239 were retrieved from the Gene Expression Omnibus (GEO) database (www.ncbi.nlm.nih.gov/geo/). MiR-124’s pan cancer analysis is conducted through online websites (www.picb.ac.cn/dbDEMC/). Bioinformatics predicted NFATc1 as the target of miR-124-3p The miRbase (www.mirbase.org/), miRDB (mirdb.org), and…

The field of bioinformatics has rapidly evolved with the advent of high-throughput sequencing technologies and other advanced experimental methods. These technologies generate massive datasets that require equally advanced computational methods for analysis. Graph databases, such as Apache Age, have emerged as powerful tools for managing and analyzing these complex datasets….

Leukemia cell culture The human acute promyelocytic leukemia cell line (NB4) and the human acute lymphocytic leukemia cell line (MOLT-4) were purchased from Cell Lines Service (Eppelheim, Germany). Leukemia cells were cultured in RPMI-1640 medium supplemented with 10% (v/v) FBS and 1% (v/v) penicillin–streptomycin (Gibco Life Technologies, Waltham, MA, USA)….

Background. Calcific aortic valve disease (CAVD) is the most common native valve disease. Valvular interstitial cell (VIC) osteogenic differentiation and valvular endothelial cell (VEC) dysfunction are key steps in CAVD progression. Circular RNA (circRNAs) is involved in regulating osteogenic differentiation with mesenchymal cells and is associated with multiple disease progression,…

DOI: 10.18129/B9.bioc.magrene   This is the development version of magrene; for the stable release version, see magrene. Motif Analysis In Gene Regulatory Networks Bioconductor version: Development (3.18) magrene allows the identification and analysis of graph motifs in (duplicated) gene regulatory networks (GRNs), including lambda, V, PPI V, delta, and bifan…

It was to analyze differentially expressed genes and their expression characteristics in ischemic cardiomyopathy (ICM) by bioinformatics and provide targets for drug therapy of ICM. For this purpose, the gene expression data of ICM in the gene expression omnibus (GEO) database were used, the differentially expressed genes between healthy myocardium…

The DUPLEX Study did not achieve the primary efficacy eGFR slope endpoint over 108 weeks of treatment Secondary and topline exploratory endpoints trended favorably for sparsentan Treatment with sparsentan resulted in a reduction of proteinuria that was sustained through 108 weeks of treatment Sparsentan was well-tolerated with a consistent safety…

RNA ligase mechanism and identification of C12orf29 by chemical proteomics using modified Ap3A probe. a Schematic display of the three-step mechanism of RNA ligation by a 5′–3′ RNA ligase. In step 1, the ligase is auto-AMPylated on the catalytic lysine using ATP as the co-substrate. In step 2, the AMP…

Background The retrograde endocannabinoid (eCB) pathway is closely associated with the etiology of major depressive disorder (MDD) at both pathophysiological and genetic levels. This study aimed to investigate the potential role of genetic mutations in the eCB pathway and underlying mechanisms in Han Chinese patients with MDD. Methods A total…

Epstein-Barr virus (EBV) is a risk factor for diffuse large B-cell lymphoma (DLBCL) and systemic lupus erythematosus (SLE). While prior research has suggested a potential correlation between SLE and DLBCL, the molecular mechanisms remain unclear. The present study aimed to explore the contribution of EBV infection to the pathogenesis of…

Abstract Diabetic patients are prone to diabetic kidney disease (DKD), which may cause cardiovascular damage, hypertension and obesity, and reduce quality of life. As a result, the life quality of patients was seriously reduced. However, the pathogenesis of diabetic kidney disease (DKD) has not been fully elucidated, and current treatments…

Introduction Gout is an inflammatory disease caused by the deposition of monosodium urate (MSU) crystals in joints and other non-joint tissues. The main clinical manifestations of gout include recurrent joint redness, swelling, heat and pain, and even joint mutilation, urinary acid nephropathy and renal failure.1,2 The incidence and prevalence of…

Introduction Ischemic cardiomyopathy (ICM), characterized by high mobility and high mortality, is so far one of the most prevalent etiologies of congestive heart failure.1 The development of left ventricular (LV) systolic dysfunction, which is typically brought on by prior acute myocardial infarction(s), or, alternatively, a sneaky process of gradual deterioration…

*For medical professionals to read and reference only Recently, the team of Dean Li Jie of the Oncology Department of Guang’anmen Hospital, China Academy of Chinese Medical Sciences , based on the immune effect of papaya saponin I, developed a new nano-drug that can achieve efficient tumor suppression by converting…

Introduction Ovarian cancer is one of the most common gynecologic malignancies with high morbidity.1 Due to its relatively asymptomatic nature, about 70% of patients are diagnosed at an advanced stage and have poor prognosis, leading to high mortality rates.2,3 The clinical treatment of ovarian cancer mainly relies on chemotherapy after…

Identification of ancestry-dependent and independent non-HLA SLE-associated variants and downstream target genes Despite the success achieved by GWAS in mapping polygenic disease risk loci in SLE, the biological implications of the majority of identified variants has remained unknown. To gain a broader view of how inherited genetic variation impacts disease…

Travere Therapeutics, Inc. (TVTX) today announced publication in The Lancet of the interim analysis of efficacy and safety data from the ongoing pivotal, Phase 3 PROTECT Study evaluating FILSPARI™ (sparsentan) in adults with IgA nephropathy (IgAN). The data are simultaneously being presented in a late-breaking trials session at the World…

enriched genes PPI network 1 It doesn’t work like that. Wherever you obtained Figure 1, it is obvious that it wasn’t done by STRING, as its style and format are completely different. If I were to guess, what’s in Figure 1 appears to be old results that were plotted manually….

Introduction Chronic obstructive pulmonary disease (COPD) is a common chronic respiratory condition that mostly occurs in middle-aged and elderly people. COPD manifests as a progressive airflow limitation associated with an abnormal lung inflammatory response.1 As a disease with high incidence, disability rate, long disease course, and multiple comorbidities, COPD has…

Trying to make a Mauve alignment with 2 sequences and keep getting error code 3 1 I’m trying to create an alignment with two sequences in Mauve (Windows) and keep getting error code 3. I tried using different formats for my sequences, but that didn’t seem to change anything. I…

Abstract Coronary artery disease (CAD) is the most common cardiovascular disorder and the leading cause of heart-related deaths in world. Increasing molecular targets have been discovered for CAD and CAD – related complications prognosis and therapy. However, there is still an urgent need to identify novel biomarkers. Therefore, we evaluated…

February 14, 2023 Ravi Lakshmanancryptocurrency / software security Malicious actors have published over 451 unique Python packages on the official Python Package Index (PyPI) repository in an attempt to infect developer systems with Clipper malware. Software supply chain security company Phylum, which looked into the libraries, said the ongoing activity…

Introduction At present, major progress has been made to prevent and treat cardiovascular disease (CVD) through lifestyle changes and drugs, but CVD is still the main cause of death in humans, especially in developed country and developing country.1 It is worth noting that the residual risk of CVD in patients…

Infectious diseases, believed to be a thing of the past only a few decades ago owing to the discovery of antibiotics, have resurfaced as an area of active research with the rampant spread of antimicrobial resistance and evolving viruses. Caused by pathogens ranging in size from viruses to worms that…

It has been reported that genes are not independent of each other, co-expressed genes may have similar biological functions, and the effect of grouping genes is relatively strong17. WGCNA algorithm, which has been widely used for studying network changes, can be used to identify network topologies and sub-networks (called modules),…

Entry EC 2.5.1.141                Enzyme                                  Name heme o synthase;ctaB (gene name);COX10 (gene name) Class Transferases;Transferring alkyl or aryl groups, other than methyl groups;Transferring alkyl or aryl groups, other than methyl groups (only sub-subclass identified to date)BRITE hierarchy Sysname (2E,6E)-farnesyl-diphosphate:protoheme IX farnesyltranstransferase Reaction(IUBMB) (2E,6E)-farnesyl diphosphate + protoheme IX + H2O = diphosphate + ferroheme…

In this study, we screened a total of eighty DEGs between DCM patients and non-DCM patients using two DCM gene expression profiles from GSE3585 and GSE84796. We performed enrichment analysis to explore the potential mechanisms underlying DCM. We also conducted immune infiltration analysis for DCM patients. Then, PPI network was…

Mechanisms of sepsis severity and mortality in COVID-19 patients To identify COVID-19 specific severity mechanisms, we initially compared the whole blood gene expression profiles associated with defined severity groups from a cohort of 124 patients recruited at various times relative to hospital admission. Patient severity was assessed using two measures,…

Wed 11 Jan – Thu 12 Jan 2023 Description This course provides an introduction to the basic theory and concepts of network analysis. Attendees will learn how to construct protein-protein interaction networks and subsequently use these to overlay large-scale data such as that obtained through RNA-Seq or mass-spec proteomics. The…

Software Figure preparation: CorelDRAW x8 (Corel); Bioinformatic analyses: R v 4.0.3 (R Foundation for Statistical Computing). Computational resources Analyses were run on a desktop computer with an Intel Core i9-10900L CPU (3.70 GHz, 10 cores, 20 threads) with 120 GB RAM running Windows 10 Pro (v21H2). Data preprocessing scRNA-seq data sets…

Zhou, P. et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 579(7798), 270–273. doi.org/10.1038/s41586-020-2012-7 (2020). Article  ADS  CAS  PubMed  PubMed Central  Google Scholar  Lipsitch, M., Swerdlow, D. L. & Finelli, L. Defining the epidemiology of Covid-19—Studies needed. N. Engl. J. Med. 382(13), 1194–1196. doi.org/10.1056/NEJMp2002125…

Cell culture Human glioblastoma cells (U87MG and U87MG-Luc) and human embryonic kidney cells (HEK293) were obtained from the American Type Culture Collection (Manassas, Va.). Cells were cultured in Dulbecco’s Modified Eagle Medium supplemented with 10% fetal bovine serum (Gibco™ Fetal Bovine Serum South America, Thermo Scientific Fisher-US), 2 mM l-glutamine, 50 U/ml…

DOI: 10.18129/B9.bioc.HPiP     Host-Pathogen Interaction Prediction Bioconductor version: Release (3.15) HPiP (Host-Pathogen Interaction Prediction) uses an ensemble learning algorithm for prediction of host-pathogen protein-protein interactions (HP-PPIs) using structural and physicochemical descriptors computed from amino acid-composition of host and pathogen proteins.The proposed package can effectively address data shortages and data…

What is the PPI network? A protein-protein interaction (PPI) network represents a platform by which we have this chance to systematically identify disease-related genes from the relations between genes with similar functions. What is virus host interaction? Definition. Virus–host interactions are the viral and host processes that occur during viral…

Acute lung injury (ALI) is a severe form of sepsis that is associated with a high rate of morbidity and death in critically ill individuals. The emergence of ALI is the result of several factors at work. Case mortality rates might range from 40% to 70%. Researchers have discovered that…

1Department of Orthopedics, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, People’s Republic of China; 2Department of Pediatrics, The Shanxi Medical University, Taiyuan, Shanxi, People’s Republic of China Correspondence: Jun Qian, Department of Orthopedics, The First Affiliated Hospital of Anhui Medical University, 218 Jixi Road, Hefei, 230022, Anhui,…

Workflow Platforms for Systems Genetics eQTL Platforms eQTL Viewer Mouse Genome Informatics: Phenotypes, Alleles & Disease Models PhenoGen Informatics (CO U) eXtensible Genotype And Phenotype platform (XGAP) MOLGENIS & MetaNetwork, Swertz & Jansen, U Groningen Weighted Gene Co-expression Network Analysis (WGCNA), Horvath, UCLA iPlant Sage Bionetworks Repository: Synapse GenomeSpace Institute…

This article was originally published here Hematology. 2022 Dec;27(1):280-292. doi: 10.1080/16078454.2022.2040123. ABSTRACT PURPOSE: While the prognosis of multiple myeloma (MM) has significantly improved over the last decade because of new treatment options, it remains incurable. Aetiological explanations and biological targets based on genomics may provide additional help for rational disease…

Introduction Acute pancreatitis (AP) is a common disease found in clinics, and requires urgent Hospital admission. The incidence of AP is increasing in recent years worldwide.1 The patients with AP increased from 1,727,789.3 to 2,814,972.3 between 1990 and 2019 in 204 countries and territories.2 Meanwhile, nearly 20% of AP patients…

Abstract The cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) signaling exert essential regulatory function in microbial-and onco-immunology through the induction of cytokines, primarily type I interferons. Recently, the aberrant and deranged signaling of the cGAS-STING axis is closely implicated in multiple sterile inflammatory diseases, including heart failure, myocardial infarction,…

doi: 10.1007/s12032-021-01642-3. Affiliations Expand Affiliations 1 Department of Blood Transfusion, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China. 2 Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China. 3 Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China. 4 Department of Blood Transfusion, Nanfang Hospital, Southern…

Introduction Keloid is excessive fibrosis of the skin that extends beyond the area of injury and does not regress.1 Keloid can occur in the joints and mouth after several years of severe injury, including burns, chemical injury, wound, and surgical incision.2 Keloids on the joints affect the quality of life,…

Background: Circular RNAs (circRNAs) have been demonstrated to be closely related to the carcinogenesis of human cancer in recent years. However, the molecular mechanism of circRNAs in the pathogenesis of hepatocellular carcinoma (HCC) has not been fully elucidated. We aimed to identify critical circRNAs and explore their potential regulatory network…

Significance Hairpin pyrrole-imidazole (Py-Im) polyamides can be programmed to bind a broad repertoire of DNA sequences. Py-Im small molecules can be used to target cancer-specific coding regions and block transcription elongation. This transcription blockage by Py-Im cannot be rescued by transcription elongation factors, such as TFIIS. The mechanism by which…

Summary Background Inter-individual variability during sepsis limits appropriate triage of patients. Identifying, at first clinical presentation, gene expression signatures that predict subsequent severity will allow clinicians to identify the most at-risk groups of patients and enable appropriate antibiotic use. Methods Blood RNA-Seq and clinical data were collected from 348 patients…

Introduction Kidney cancer is one of the most commonly diagnosed tumors around the globe.1 According to the statistics from the World Health Organization, annually, there are more than 140,000 RCC-related deaths.2 ccRCC is the most typical subtype of kidney cancer and contributes to the majority of kidney cancer-related deaths.3,4 Until…

Introduction Tuberculosis (TB) is considered to be one of the top ten causes of death in the world, about a quarter of the world’s population is infected with M. tuberculosis.1 The World Health Organization (WHO) divides tuberculosis into pulmonary tuberculosis (PTB) and extra-pulmonary tuberculosis (EPTB). Although breakthroughs have been made…

This article was originally published here Dis Markers. 2021 Dec 10;2021:1776567. doi: 10.1155/2021/1776567. eCollection 2021. ABSTRACT BACKGROUND: This current study applied bioinformatics analysis to reveal the crosstalk between venous thromboembolism (VTE) and periodontitis, as well as the potential role of immune-related genes in this context. METHODS: Expression data were downloaded…

Background Primary hyperaldosteronism (PA) is characterized by spontaneous secretion of excessive aldosterone and inhibition of plasma renin activity.1 The pathogenesis of adrenal aldosterone-producing adenoma (APA) involves the abnormal proliferation of adrenal cortex cells and the excessive secretion of aldosterone, accounting for nearly 30% of PA. Excessive secretion of aldosterone can…

Introduction Renal cell carcinoma (RCC) accounts for approximately 2–3% of all malignant tumors, and its prevalence is rising. Metastatic RCC accounts for 25–30% of all RCC cases, and has an exceedingly poor prognosis.1 In 2020, among approximately 430,000 newly discovered cases of RCC, 179,000 died.2 Clear cell renal cell carcinoma…

Introduction According to the cancer statistics reported in 2020, hepatocellular carcinoma (HCC) is the main type of Primary Carcinoma of the Liver and the second leading causes of cancer-related death globally, with a five-year survival rate < 20%.1 Currently, surgical resection, a standard therapy for HCC, contributes to the prognosis…

Introduction Alzheimer’s disease (AD) ranks first among the common dementia type of the world. According to epidemiological investigation from the International Alzheimer’s disease association, about 45 million people has been suffered from AD, and the number is expected to increase to 131 million in 2050.1 Despite the widespread prevalence of…

Background Female breast cancer has surpassed lung cancer as the most commonly diagnosed cancer. Despite the dramatic improvement in breast cancer prognosis due to recent therapeutic advances, such as more effective adjuvant and neo-adjuvant chemotherapies, together with more radical and safer surgery, advances in early diagnosis and treatment over the…

This article was originally published here Bioinformatics. 2021 Dec 2:btab812. doi: 10.1093/bioinformatics/btab812. Online ahead of print. ABSTRACT MOTIVATION: Clustering spatial-resolved gene expressions is an essential analysis to reveal gene activities in the underlying morphological context by their functional roles. However, conventional clustering analysis does not consider gene expression co-localizations in…

Background: Circular RNA (circRNA) has been receiving increased attention in the research of atrial fibrillation (AF). Our study aims to find potential circRNAs and identify the circRNA-miRNA-mRNA regulatory network in AF based on bioinformatics analysis. Methods: GSE129409 was retrieved from the Gene Expression Omnibus (GEO) database, and we used R…

Introduction Crohn’s disease (CD) and ulcerative colitis are chronic inflammatory disorders of the gastrointestinal tract, with symptoms evolving in a relapsing and remitting manner that comprise the term inflammatory bowel disease (IBD).1 CD is characterized by the involvement of all parts of the intestine, the most common being the terminal…

1Department of Cardiology, Xiangtan Central Hospital, Xiangtan, Hunan, People’s Republic of China; 2Department of Cardiology, Guangxi Cardiovascular Institute, The First Affiliated Hospital of Guangxi Medical University, Guangxi, People’s Republic of China; 3Department of Critical Care Medicine, Zhuzhou Central Hospital, Zhuzhou, Hunan, People’s Republic of China Correspondence: Yiqian ZengDepartment of Critical…

Comput Biol Med. 2021 Nov 20:105043. doi: 10.1016/j.compbiomed.2021.105043. Online ahead of print. ABSTRACT BACKGROUND: Clear cell renal cell carcinoma (ccRCC) is one of the common subtypes of kidney cancer. Circular RNAs (circRNAs) act as competing endogenous RNAs (ceRNAs) to affect the expression of microRNAs (miRNAs), and hence the expression of…

1 Introduction Lung cancer is the leading cause of cancer-related deaths worldwide, with adenocarcinoma as the most common histological subtype.1 In recent years, epidermal growth factor receptor-tyrosine kinase inhibitors (EGFR-TKIs), such as gefitinib (first generation) and osimertinib (third generation), have been widely used for lung adenocarcinoma patients harboring activated EGFR…

Severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) is a positive-strand RNA virus, which appears spherical under a transmission electron microscope. Many studies have shown that SARS-CoV-2 infects host cells via the interaction between the viral spike protein and the host receptor, angiotensin-converting enzyme II (ACE2). SARS-CoV-2 can spread through…

Introduction Polycystic ovary syndrome (PCOS) is a common endocrine metabolic disorder in women of childbearing age.1 PCOS patients are typically characterized by androgen excess, polycystic ovaries and anovulation, and are often accompanied by insulin resistance and obesity.2 Consequently, patients with this syndrome not only suffer from infertility,3 but also have…

Broaden your search Bioinformatics, Full Time, Govt., Bethesda, Maryland 1 Life Sciences, Full Time, Govt., Senior Scientist, Bethesda, Maryland 1 Bioinformatics, Full Time, Govt., Senior Scientist, Maryland 1 Refine your search To see more jobs like this, please sign up…

The artificial intelligence (AI) revolution in the field of protein structure prediction continues. At the end of 2020, the new generation of AlphaFold (AlphaFold2) developed by DeepMind has solved the major challenges in the biological field for decades and achieved a major breakthrough in accurately predicting the 3D structure of…

Introduction Atrial fibrillation (AF) is the most common type of arrhythmia in clinical practice, with global prevalence continuing to increase primarily with age.1 In China, 6.5 persons out of every thousand suffer from AF, and there are about 3.9 million patients with AF who are over 60 years old, but…

Entry EC 2.6.1.57                 Enzyme                                  Name aromatic-amino-acid transaminase;aromatic amino acid aminotransferase;aromatic aminotransferase;ArAT Class Transferases;Transferring nitrogenous groups;TransaminasesBRITE hierarchy Sysname aromatic-amino-acid:2-oxoglutarate aminotransferase Reaction(IUBMB) an aromatic amino acid + 2-oxoglutarate = an aromatic oxo acid + L-glutamate [RN:R03120] Reaction(KEGG) R03120 > R00694 R00734 R10845; (other) R01731 R07396 Reaction Substrate aromatic amino acid [CPD:C01021]; 2-oxoglutarate [CPD:C00026] Product…

Introduction Many postmenopausal women suffer from postmenopausal osteoporosis (PMO). A survey of 3247 Italian postmenopausal women found that according to bone mineral density (BMD) diagnostic criteria, the prevalence of osteoporosis was 36.6%.1 PMO patients may suffer from chronic pain and fractures, and as a result their quality of life is…

Broaden your search Bioinformatics, Pearl River, New York 1 Life Sciences, Pharma, Pearl River, New York 15 Bioinformatics, All Industry, Pearl River, New York 1 Bioinformatics, Pharma, New York 1 Refine your search To see more jobs like…

Introduction Atrial fibrillation (AF) is the most common clinically sustained cardiac rhythm disorder. There is a high prevalence of AF all over the world, the highest in North America, Europe, China, and Southeast Asia, with approximately 270–360 cases per 100,000 people.1 Due to the lack of understanding of the pathogenesis…

Jia Xu,1 Ming-Ying Zhang,2 Wei Jiao,1 Cong-Qi Hu,1 Dan-Bin Wu,2 Jia-Hui Yu,1 Guang-Xing Chen2,3 1First Clinical Medical School, Guangzhou University of Chinese Medicine, Guangzhou, 510405, Guangdong, People’s Republic of China; 2Department of Rheumatology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, 510405, Guangdong, People’s Republic of China;…

This article was originally published here Transl Androl Urol. 2021 Sep;10(9):3604-3619. doi: 10.21037/tau-21-326. ABSTRACT BACKGROUND: Bladder cancer (BLCA) is the most prevalent tumor affecting the urinary system, and has contributed to a rise in morbidity and mortality rates. Herein, we sought to identify the methylation-driven genes (MDGs)of BLCA in an…

This article was originally published here Biomed Res Int. 2021 Oct 11;2021:5516218. doi: 10.1155/2021/5516218. eCollection 2021. ABSTRACT BACKGROUND: The aim of this study was to identify potential key genes, proteins, and associated interaction networks for the development of lung cancer in nonsmoking women through a bioinformatics approach. METHODS: We used…

This article was originally published here Front Cell Dev Biol. 2021 Oct 4;9:722671. doi: 10.3389/fcell.2021.722671. eCollection 2021. ABSTRACT Atrial fibrillation (AF)/paroxysmal AF (PAF) is the main cause of cardiogenic embolism. In recent years, the progression from paroxysmal AF to persistent AF has attracted more and more attention. However, the molecular…

Introduction As one of the most frequent causes of cancer deaths across the globe, liver cancer, characterized by high mortality, recurrence, metastasis and poor prognosis, is the only one of the top five deadliest cancers to have an annual percentage increase in occurrence.1 Surgery, local destructive therapies, and liver transplantation…

Abstract Oral squamous cell carcinoma (OSCC) is the most common malignant epithelial neoplasm and anatomical subtype of head and neck squamous cell carcinoma (HNSCC) with an average 5-year survival rate of less than 50%. To improve the survival rate of OSCC, the discovery of novel anti-cancer drugs is urgently needed….

This article was originally published here BMC Med Genomics. 2021 Oct 7;14(1):241. doi: 10.1186/s12920-021-01092-w. ABSTRACT BACKGROUND: Despite papillary renal cell carcinoma (pRCC) being the second most common type of kidney cancer, the underlying molecular mechanism remains unclear. Targeted therapies in the past have not been successful because of the lack…

Introduction Helicobacter pylori is a common pathogen that infects nearly 50% of the global population.1 Infection with this pathogen causes chronic gastritis, which can cause chronic gastroduodenal diseases such as gastritis, gastric ulcer, duodenal ulcer, gastric cancer, and gastric mucosa-associated lymphoid tissue (MALT) B-cell lymphoma.2 Although H. pylori is the…

Entry EC 2.7.1.90                 Enzyme                                  Name diphosphate—fructose-6-phosphate 1-phosphotransferase;6-phosphofructokinase (pyrophosphate);pyrophosphate-fructose 6-phosphate 1-phosphotransferase;inorganic pyrophosphate-dependent phosphofructokinase;inorganic pyrophosphate-phosphofructokinase;pyrophosphate-dependent phosphofructo-1-kinase;pyrophosphate-fructose 6-phosphate phosphotransferase Class Transferases;Transferring phosphorus-containing groups;Phosphotransferases with an alcohol group as acceptorBRITE hierarchy Sysname diphosphate:D-fructose-6-phosphate 1-phosphotransferase Reaction(IUBMB) diphosphate + D-fructose 6-phosphate = phosphate + D-fructose 1,6-bisphosphate [RN:R00764] Reaction(KEGG) Substrate diphosphate [CPD:C00013]; D-fructose 6-phosphate [CPD:C00085] Product phosphate [CPD:C00009]; D-fructose…

How to calculate the risk ratio(Enrichment) of mutations on interaction interfaces 0 Hi there, I’m doing a study about the impact of mutations on the interaction interface of proteins, and I need to calculate the risk ratio between the disease group and the control group. I found a published paper…

This paper is published in… By Zhou Yaoqi research group of Shenzhen Graduate School of Peking University and Yang Yuedong research group of Sun Yat sen University Bioinformatics Articles on . Address of thesis ：https://doi.org/10.1093/bioinformatics/btab643 Abstract protein – Protein interactions （PPI） It plays a vital role in many biological processes…

This article was originally published here Acta Biochim Biophys Sin (Shanghai). 2021 Sep 24:gmab128. doi: 10.1093/abbs/gmab128. Online ahead of print. ABSTRACT Multiple myeloma (MM) is an incurable disease characterized by malignant plasma cell clonal expansion in the bone marrow; therefore, inhibiting the proliferation of plasma cells is an important approach…

Introduction Intestinal ischemia-reperfusion (II/R) injury is a severe clinical complication common in the Intensive Care Unit (ICU). It is associated with high morbidity and mortality.1 Usually, this problem is followed by various causes, including sepsis, shock, trauma, and so on.2 Intestinal ischemia-reperfusion injury destroys intestinal tissue and impairs the function…

PPI-Network igraph for tissue-specific data 0 I am new to bioinformatics in general and would really appreciate some help with the project Im working on. My data of protein-protein interactions is constructed in a table (stored in MySQL) with binary information about tissue-specificity. Now I am trying to create an…

I am having trouble running the blastp command. When I run this command against the Swiss-prot database installed from the NCBI i get this error $ blastp -db swissprot -query Ecoli_rpoB.fasta -out TEST15.txt BLAST Database error: Error: Not a valid version 4 database. However, when I create my own database…

Introduction Thyroid cancer (TC) is a common endocrine malignancy with a rapidly increasing incidence worldwide, and the estimated new cases and deaths are notably higher in women than in men.1 Papillary thyroid carcinoma (PTC) is identified as the most common pathological type of TC, and accounts for approximately 80–85% of…

DOI: 10.18129/B9.bioc.PPInfer     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see PPInfer. Inferring functionally related proteins using protein interaction networks Bioconductor version: 3.12 Interactions between proteins occur in many, if not most, biological processes. Most proteins perform their functions in networks associated…

This article was originally published here Comput Math Methods Med. 2021 Aug 28;2021:9946015. doi: 10.1155/2021/9946015. eCollection 2021. ABSTRACT It is urgent to identify novel biomarkers for prostate cancer (PCa) prognosis and to understand the mechanisms regulating the tumorigenesis for PCa treatment. In this study, GSE17951 and TCGA were used to…

Network analysis using distinct centrality measurements 0 Hello to everyone, I have question regarding to network analysis. Currently, I’m conducting this kind of analysis using data retrieved from STRING db to obtain highly central nodes. I have re-constructed the network in R using the igraph package to subsequently proceed with…

GitHub – HaoWuLab-Bioinformatics/wu-group: ECSWalk Files Permalink Failed to load latest commit information. Type Name Latest commit message Commit time ECSWalk: A carcinogenic driver module detection method based on a network model. Data used in this study: In our research, we used data processed by Rafsan Ahmed, et al. and Mark…

Introduction Mirror-image pain (MIP) is a mysterious pain phenomenon which is accompanied with many clinical pain conditions.1 MIP develops from the healthy body region which is contralateral to the actual injured site.1–3 MIP is typically characterized by increased mechanical hypersensitivity on the uninjured mirror-image body side.4 It can be triggered…

NEW YORK – A new method for profiling protein-protein interactions (PPIs) using next-generation sequencing as a readout has the potential to reveal thousands of previously undiscovered combinations in human cells. The method, called PROPER-seq (protein-protein interaction sequencing), tags proteins with RNA barcodes that form chimeric sequences when brought into proximity with…

Problem of visualizing results of PPI network 0 Hi,I want to visualize my PPI network into cytoscape or Network analyst .But my ppI node are 661 and edges are 680 and seeds are 15.So i feel problem of visualizing it into cytoscape or Network analyst.Because of huge number of nodes…

Abstract A critical challenge for microbiology and medicine is how to cure infections by bacteria that survive antibiotic treatment by persistence or tolerance. Seeking mechanisms behind such high survival, we developed a forward-genetic method for efficient isolation of high-survival mutants in any culturable bacterial species. We found that perturbation of…

Introduction Helicobacter pylori, an infectious agent of human chronic active gastritis and also associated with other gastric ailments such as peptic ulcer, gastric cancer, and mucosa-associated lymphoid tissue lymphoma.1 Clarithromycin is considered the best option among other antibiotics for the management of this bacterial infection.2 However, increasing resistance against this…

How can I get the exact 3D structure of the protein to use the PDB file for PPI docking 1 I am working on an uncharacterized protein, and I need to know its PPI with rna polymrase in humans. Please, how can I get the exact 3D structure of the…